Hi Mark and Rolf,
This works wonderfully! Thank you very much for your great help, :)
Jim
On Fri, 2 Oct 2009 08:24:23 +0100, Mark Jenkinson <[log in to unmask]>
wrote:
>Hi,
>
>Yes, you can get this information from FLIRT.
>Just do:
> flirt -in resampled_image -ref refimage -schedule measurecost1.sch
>You can also select the similarity metric you want with -cost ...
>
>The measurecost1.sch file has been posted on the list before, but
>I'm attaching another copy here. Just save it (as plain text)
>somewhere and give the full path in the command above.
>
>The cost value is the first number printed. If you want to
>automatically
>select only this then you can do:
> flirt .... | head -1 | cut -f1 -d' '
>with the above flirt command.
>
>All the best,
> Mark
>
>
>
>
>
>
>On 2 Oct 2009, at 07:26, Rolf Heckemann wrote:
>
>> Hi Jim
>>
>> I'm not sure if there is an FSL tool. In IRTK, there is "evaluation",
>> which gives you mutual information and a host of other similarity
>> measures for a pair of images.
>>
>> Hope that helps
>>
>> Rolf
>>
>>
>> On Fri, Oct 02, 2009 at 04:36:55AM +0100, Jim Li wrote:
>>> Hi Rolf,
>>>
>>> Thanks a lot for your help. As you said, the ".mat" can catch very
>>> gross
>>> failures of registration. That helps.
>>>
>>> I always visually inspect the registrations, like what Mark
>>> suggested. By so
>>> doing I can have an opinion of which registration works better.
>>> Let's say I
>>> have two image volumes a and b. Using a as reference, I register b
>>> to a with
>>> one registration method and created a volume c; then I do the same
>>> thing
>>> with another registration method and created a volume d. Now I want
>>> to
>>> calculate the mutual information between a and c, as well as the
>>> mutual
>>> information between a and d. Is there a command to use in FSL to do
>>> this?
>>>
>>> I understand what Mark said that change of such numbers does not
>>> necessarily indicate a change in the quality of the alignment. I'm
>>> just curious
>>> and want to get such numbers to play with them. That's all.
>>>
>>>
>>> Jim
>>>
>>> On Tue, 29 Sep 2009 15:57:48 +0100, Rolf Heckemann
>>> <[log in to unmask]> wrote:
>>>
>>>> Hi Jim
>>>>
>>>> When you run FLIRT with default settings to register a pair of
>>>> images
>>>> (no matter whether they are from the same subject or different
>>>> ones),
>>>> the output represents the optimal alignment as measured by the
>>>> correlation ratio. You can set an option for FLIRT to use a
>>>> different
>>>> cost function, e.g. mutual information. This then becomes the
>>>> measure
>>>> of "goodness", and FLIRT manipulates the alignment parameters until
>>>> this value becomes as "good" as possible.
>>>>
>>>> Perhaps you can see now why it is difficult to answer your question.
>>>>
>>>> If you want to catch very gross failures, such as a pair of images
>>>> not
>>>> matching at all after registration, and you want to avoid opening
>>>> and
>>>> looking at each aligned pair, then I suggest you have a look at
>>>> flirt's .mat output. The numbers in there describe the
>>>> transformation. If you have a large number of .mat files, you may
>>>> recognize failed registrations as outliers in one or more of these
>>>> numbers.
>>>>
>>>> Hope that helps
>>>>
>>>> Rolf
>>>>
>>>>
>>>> On Tue, Sep 29, 2009 at 03:35:54PM +0100, Jim Li wrote:
>>>>> Hi Mark,
>>>>>
>>>>> Thanks a lot for the message, :)
>>>>>
>>>>> You know, I'm not doing image registration on different subjects.
>>>>> I have
>>> the
>>>>> same subject whose T2-weighted images and b0 images were done on
>>>>> the
>>>>> same day, and I tried two different ways to register the two image
>>> volumes. I
>>>>> just want to get some values to quantify the registration and see
>>>>> if there's
>>> a
>>>>> pattern. Could you suggest some ready-to-use script? Will
>>>>> fslmaths work?
>>>>>
>>>>> Thanks a lot,
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>>
>>>>> On Tue, 29 Sep 2009 08:17:52 +0100, Mark Jenkinson
>>>>> <[log in to unmask]> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm afraid that there is no easy way to compare the quality of
>>>>>> registrations for different subjects. You can use mutual
>>>>>> information
>>>>>> or other metrics to compare the quality of two different
>>>>>> registrations
>>>>>> of the same images (this is how the registration works), but the
>>>>>> values
>>>>>> are not really comparable across different registrations of
>>>>>> different
>>>>>> images/subjects, and will tend to be influenced a lot by the FOV,
>>>>>> SNR, artefact level (e.g. amount of motion) and so on. Hence a
>>>>>> larger/smaller number does not necessarily indicate a change in
>>>>>> the quality of the alignment.
>>>>>>
>>>>>> We strongly recommend you visually inspect all your registrations.
>>>>>> This is definitely the best way to assess the quality of the
>>>>>> alignment.
>>>>>>
>>>>>> All the best,
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>> On 28 Sep 2009, at 14:46, Jim Li wrote:
>>>>>>
>>>>>>> Hello everybody,
>>>>>>>
>>>>>>> I have another Newbie question about registering two image
>>>>>>> volumes
>>>>>>> of the
>>>>>>> same subject using the same modality (MRI) after using FLIRT or
>>>>>>> other scripts.
>>>>>>> Can anyone give me a hint?
>>>>>>>
>>>>>>> Basicly, other than visual inspection of the two images after
>>>>>>> registration, are
>>>>>>> there ready-to-use scripts in FSL that can quantify the overall
>>>>>>> goodness of
>>>>>>> registration? I heard people use mutual information, etc. I just
>>>>>>> want to run a
>>>>>>> command to get a number (or more) to quantify the goodness of
>>>>>>> registration...
>>>>>>>
>>>>>>> Thanks a lot, :)
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>
>>>> --
>>>> Rolf A Heckemann, MD PhD
>>>> Médecin chercheur
>>>> Fondation Neurodis
>>>> CERMEP - Imagerie du Vivant
>>>> Hôpital Neurologique Pierre Wertheimer
>>>> 59 Boulevard Pinel
>>>> 69003 Lyon
>>>>
>>>>
>>>>
>>>> 1254235444
>>>>
>>>>
>>
>> --
>> Rolf A Heckemann, MD PhD
>> Médecin chercheur
>> Fondation Neurodis
>> CERMEP - Imagerie du Vivant
>> Hôpital Neurologique Pierre Wertheimer
>> 59 Boulevard Pinel
>> 69003 Lyon
>>
>>
>>
>> 1254464487
>>
>
>
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